def test_persistence():
"""
Tests persistence of a managers jobs.
"""
staging_directory = tempfile.mkdtemp()
try:
app = Bunch(
staging_directory=staging_directory,
persistence_directory=staging_directory,
authorizer=get_authorizer(None),
dependency_manager=TestDependencyManager(),
job_metrics=Bunch(default_job_instrumenter=NULL_JOB_INSTRUMENTER),
)
assert not exists(join(staging_directory, "queued_jobs"))
queue1 = StatefulManagerProxy(
QueueManager('test', app, num_concurrent_jobs=0))
job_id = queue1.setup_job('4', 'tool1', '1.0.0')
touch_file = join(staging_directory, 'ran')
queue1.launch(job_id, 'touch %s' % touch_file)
time.sleep(.4)
assert (not (exists(touch_file)))
queue1.shutdown()
queue2 = StatefulManagerProxy(
QueueManager('test', app, num_concurrent_jobs=1))
time.sleep(1)
assert exists(touch_file)
finally:
shutil.rmtree(staging_directory)
try:
queue2.shutdown()
except:
pass
def test_persistence():
"""
Tests persistence of a managers jobs.
"""
staging_directory = tempfile.mkdtemp()
try:
app = Bunch(staging_directory=staging_directory,
persistence_directory=staging_directory,
authorizer=get_authorizer(None),
dependency_manager=TestDependencyManager(),
job_metrics=Bunch(default_job_instrumenter=NULL_JOB_INSTRUMENTER),
)
assert not exists(join(staging_directory, "queued_jobs"))
queue1 = StatefulManagerProxy(QueueManager('test', app, num_concurrent_jobs=0))
job_id = queue1.setup_job('4', 'tool1', '1.0.0')
touch_file = join(staging_directory, 'ran')
queue1.launch(job_id, 'touch %s' % touch_file)
time.sleep(.4)
assert (not(exists(touch_file)))
queue1.shutdown()
queue2 = StatefulManagerProxy(QueueManager('test', app, num_concurrent_jobs=1))
queue2.recover_active_jobs()
time.sleep(1)
assert exists(touch_file)
finally:
shutil.rmtree(staging_directory)
try:
queue2.shutdown()
except:
pass
def _app():
with temp_directory() as staging_directory:
app = Bunch(
staging_directory=staging_directory,
persistence_directory=staging_directory,
authorizer=get_authorizer(None),
dependency_manager=TestDependencyManager(),
job_metrics=Bunch(default_job_instrumenter=NULL_JOB_INSTRUMENTER),
)
yield app
def _app():
with temp_directory() as staging_directory:
app = Bunch(
staging_directory=staging_directory,
persistence_directory=staging_directory,
authorizer=get_authorizer(None),
dependency_manager=TestDependencyManager(),
job_metrics=Bunch(default_job_instrumenter=NULL_JOB_INSTRUMENTER),
)
yield app
def __setup_tool_config(self, conf):
"""
Setups toolbox object and authorization mechanism based
on supplied toolbox_path.
"""
tool_config_files = conf.get("tool_config_files", None)
if not tool_config_files:
# For compatibity with Galaxy, allow tool_config_file
# option name.
tool_config_files = conf.get("tool_config_file", None)
toolbox = None
if tool_config_files:
toolbox = ToolBox(tool_config_files)
else:
log.info(NOT_WHITELIST_WARNING)
self.toolbox = toolbox
self.authorizer = get_authorizer(toolbox)
def __setup_tool_config(self, conf):
"""
Setups toolbox object and authorization mechanism based
on supplied toolbox_path.
"""
tool_config_files = conf.get("tool_config_files", None)
if not tool_config_files:
# For compatibity with Galaxy, allow tool_config_file
# option name.
tool_config_files = conf.get("tool_config_file", None)
toolbox = None
if tool_config_files:
toolbox = ToolBox(tool_config_files)
else:
log.info(NOT_WHITELIST_WARNING)
self.toolbox = toolbox
self.authorizer = get_authorizer(toolbox)
def test_allow_any_authorization():
authorizer = get_authorizer(None)
authorization = authorizer.get_authorization('tool1')
authorization.authorize_setup()
authorization.authorize_tool_file('cow',
'#!/bin/bash\necho "Hello World!"')
def setUp(self):
self.toolbox = get_test_toolbox()
self.authorizer = get_authorizer(self.toolbox)
def test_allow_any_authorization():
authorizer = get_authorizer(None)
authorization = authorizer.get_authorization('tool1')
authorization.authorize_setup()
authorization.authorize_tool_file('cow', '#!/bin/bash\necho "Hello World!"')
def setUp(self):
self.toolbox = get_test_toolbox()
self.authorizer = get_authorizer(self.toolbox)